FastQC Summary

Summary statistics for all libraries
Filename Total Flagged As Poor Quality Sequence Length %GC
Ps2Ex3M1_Heter_6month_07_07_2016_F3_80_Fem_R1.fastq.gz 33,616,951 0 35-150 46
Ps2Ex3M1_Heter_6month_07_07_2016_F3_80_Fem_R2.fastq.gz 33,616,951 0 35-150 46
Ps2Ex3M1_Heter_6month_07_07_2016_F3_81_Fem_R1.fastq.gz 33,633,649 0 35-150 46
Ps2Ex3M1_Heter_6month_07_07_2016_F3_81_Fem_R2.fastq.gz 33,633,649 0 35-150 46
Ps2Ex3M1_Heter_6month_07_07_2016_F3_84_Fem_R1.fastq.gz 32,688,932 0 35-150 50
Ps2Ex3M1_Heter_6month_07_07_2016_F3_84_Fem_R2.fastq.gz 32,688,932 0 35-150 51
Ps2Ex3M1_Heter_6month_07_07_2016_F3_89_Fem_R1.fastq.gz 35,599,860 0 35-150 45
Ps2Ex3M1_Heter_6month_07_07_2016_F3_89_Fem_R2.fastq.gz 35,599,860 0 35-150 46
Ps2Ex3M1_Hom_6month_07_07_2016_F3_78_Fem_R1.fastq.gz 33,710,024 0 35-150 45
Ps2Ex3M1_Hom_6month_07_07_2016_F3_78_Fem_R2.fastq.gz 33,710,024 0 35-150 45
Ps2Ex3M1_Hom_6month_07_07_2016_F3_82_Fem_R1.fastq.gz 30,045,929 0 35-150 45
Ps2Ex3M1_Hom_6month_07_07_2016_F3_82_Fem_R2.fastq.gz 30,045,929 0 35-150 45
Ps2Ex3M1_Hom_6month_07_07_2016_F3_83_Fem_R1.fastq.gz 32,193,899 0 35-150 46
Ps2Ex3M1_Hom_6month_07_07_2016_F3_83_Fem_R2.fastq.gz 32,193,899 0 35-150 46
Ps2Ex3M1_Hom_6month_07_07_2016_F3_85_Fem_R1.fastq.gz 33,316,915 0 35-150 46
Ps2Ex3M1_Hom_6month_07_07_2016_F3_85_Fem_R2.fastq.gz 33,316,915 0 35-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_79_Fem_R1.fastq.gz 26,558,035 0 35-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_79_Fem_R2.fastq.gz 26,558,035 0 35-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_86_Fem_R1.fastq.gz 31,048,376 0 35-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_86_Fem_R2.fastq.gz 31,048,376 0 35-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_88_Fem_R1.fastq.gz 32,895,183 0 35-150 46
Ps2Ex3M1_WT_6month_07_07_2016_F3_88_Fem_R2.fastq.gz 32,895,183 0 35-150 47
Ps2Ex3M1_WT_6month_07_07_2016_F3_95_Fem_R1.fastq.gz 30,558,083 0 35-150 45
Ps2Ex3M1_WT_6month_07_07_2016_F3_95_Fem_R2.fastq.gz 30,558,083 0 35-150 45

Read Totals

Library Sizes ranged between 26,558,035 and 35,599,860 reads.

Read totals for each library. Duplicated reads are conventionally an high overestimate at this point.

FastQC Summary

Summary of FastQC flags for each parameter

Per Base Sequence Quality

Heatmap showing mean base qualities for each library

Per Sequence Quality Scores

Heatmap showing mean sequence qualities for each library

Per Base Sequence Content

Heatmap of summed base distributions along each read

Per Sequence GC Content

GC Content Heatmap normalised to theoretical GC content in the Drerio Transcriptome

GC Content Distributions for all reads showing theoretical GC content from the Drerio Transcriptome

Sequence Length Distribution

Sequence Duplication Levels

Adapter Content

Universal Adapter Content

Overrepresented Summary

Total overrepresented sequences for each library

Overrepresented Sequences

Summary of the most overrepresented sequences in all files. A maximum of 30 sequences are shown
Sequence Total Present In Overall Percentage Max_Percentage Possible_Source
GGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATC 3,249,815 12 0.4211069% 1.115385% No Hit
GTGGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGC 3,215,637 12 0.4166781% 1.761673% No Hit
CTCCTGAAAAGGTTGTATCCTTTGTTAAAGGGGCTGTACCCTCTTTAACT 3,080,468 12 0.3991631% 1.132295% No Hit
CGAGAGGCTCTAGTTGATATACTACGGCGTAAAGGGTGGTTAAGGAACAA 2,810,794 12 0.3642191% 1.037056% No Hit
CTGGGGGAGCGGCCGCCCCGCGGCGCCCCCTCTCGTTCCCGTCTCCGGAG 2,476,229 10 0.3208666% 1.670850% No Hit
GTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCATCT 2,327,892 12 0.3016453% 0.807325% No Hit
CCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATCC 2,165,613 12 0.2806174% 1.332439% No Hit
CCTCCTTCAAGTATTGTTTCATGTTACATTTTCGTATATTCTGGGGTAGA 2,112,453 12 0.2737289% 0.835466% No Hit
GGGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTT 1,763,107 11 0.2284611% 0.690390% No Hit
CCCGCTGTATTACTCAGGCTGCACTGCAGTGTCTATTCACAGGCGCGATC 1,349,526 12 0.1748698% 0.794529% No Hit
GGCCTCTAGCATCTAAAAGCGTATAACAGTTAAAGGGCCGTTTGGCTTTA 1,304,192 11 0.1689955% 0.531636% No Hit
CTGGGAGATGAATAAAAGTTCAGCTTCGTACACCCCAAATTAAAAAATTA 1,294,226 10 0.1677041% 0.481060% No Hit
GGCCCGGCGCACGTCCAGAGTCGCCGCCGCACACCGCAGCGCATCCCCCC 1,286,449 9 0.1666964% 0.954118% No Hit
GGCCCGGCGCACGTCCAGAGTCGCCGCCGCGCACCGCAGCGCATCCCCCC 1,229,243 9 0.1592837% 0.791561% No Hit
GGGTTCAGGTAATTAATTTAAAGCTACTTTCGTGTTTGGGCCTCTAGCAT 1,201,907 12 0.1557416% 0.800512% No Hit
GGGGGAGCGGCCGCCCCGCGGCGCCCCCTCTCGTTCCCGTCTCCGGAGCG 1,194,580 9 0.1547921% 0.849190% No Hit
GGGGTGTACGAAGCTGAACTTTTATTCATCTCCCAGACAACCAGCTATTG 1,159,508 12 0.1502476% 1.095062% No Hit
GCCCACTACGACAACGTGTTTTGTAAATTATGATCTTTATTCTCCTGAAA 1,124,368 10 0.1456942% 0.439807% No Hit
CAGTGGCGTGCGCCTGTAATCCAAGCTACTGGGAGGCTGAGGCTGGCGGA 1,075,489 11 0.1393605% 0.656409% No Hit
CGGGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGG 1,023,269 12 0.1325939% 0.726131% No Hit
GCCTATTTAACTTAGGGCCAACCCGTCTCTGTGGCAATAGAGTGGGAAGA 954,310 12 0.1236583% 0.481652% No Hit
CTCCTTCAAGTATTGTTTCATGTTACATTTTCGTATATTCTGGGGTAGAA 930,706 10 0.1205997% 0.398321% No Hit
GAAGAAATTCATAATTCTGACAATAATATCTTACTTCCCTAAAAATACCA 921,563 10 0.1194150% 0.380088% No Hit
CTTAGACGACCTGGTAGTCCAAGGCTCCCCCAGGAGCACCATATCGATAC 912,984 11 0.1183033% 0.542948% No Hit
ATAAAAGTTCAGCTTCGTACACCCCAAATTAAAAAATTAAATTTAATTTA 907,268 9 0.1175626% 0.427929% No Hit
GGGGTAACGATGTCTGTTGTGGATTTTTCTCAGTTTTTAACTCACATTGC 868,461 10 0.1125341% 0.350438% No Hit
CTCTAGTTGATATACTACGGCGTAAAGGGTGGTTAAGGAACAATGTAAAA 860,273 12 0.1114731% 0.437826% No Hit
GGTCGGGTGGGTGGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGGAC 822,637 11 0.1065962% 0.449608% No Hit
CAGCCTATTTAACTTAGGGCCAACCCGTCTCTGTGGCAATAGAGTGGGAA 768,730 12 0.0996110% 0.524002% No Hit
CGGGTCGGGTGGGTAGCCGGCATCACCGCGGACCTCGGGCGCCCTTTTGG 765,610 12 0.0992068% 0.564748% No Hit

Session Information

R version 3.6.1 (2019-07-05)

Platform: x86_64-pc-linux-gnu (64-bit)

locale: LC_CTYPE=en_AU.UTF-8, LC_NUMERIC=C, LC_TIME=en_AU.UTF-8, LC_COLLATE=en_AU.UTF-8, LC_MONETARY=en_AU.UTF-8, LC_MESSAGES=en_AU.UTF-8, LC_PAPER=en_AU.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_AU.UTF-8 and LC_IDENTIFICATION=C

attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base

other attached packages: readr(v.1.3.1), stringr(v.1.4.0), magrittr(v.1.5), scales(v.1.1.0), pander(v.0.6.3), kableExtra(v.1.1.0), dplyr(v.0.8.3), ngsReports(v.1.1.4), tibble(v.2.1.3), ggplot2(v.3.2.1) and BiocGenerics(v.0.32.0)

loaded via a namespace (and not attached): bitops(v.1.0-6), matrixStats(v.0.55.0), lubridate(v.1.7.4), webshot(v.0.5.1), RColorBrewer(v.1.1-2), httr(v.1.4.1), GenomeInfoDb(v.1.22.0), tools(v.3.6.1), backports(v.1.1.5), R6(v.2.4.1), lazyeval(v.0.2.2), colorspace(v.1.4-1), withr(v.2.1.2), tidyselect(v.0.2.5), compiler(v.3.6.1), rvest(v.0.3.5), Biobase(v.2.46.0), Cairo(v.1.5-10), flashClust(v.1.01-2), xml2(v.1.2.2), DelayedArray(v.0.12.0), plotly(v.4.9.1), ggdendro(v.0.1-20), labeling(v.0.3), digest(v.0.6.22), Rsamtools(v.2.2.1), rmarkdown(v.1.17), XVector(v.0.26.0), pkgconfig(v.2.0.3), htmltools(v.0.4.0), fastmap(v.1.0.1), FactoMineR(v.1.42), highr(v.0.8), htmlwidgets(v.1.5.1), rlang(v.0.4.1), rstudioapi(v.0.10), shiny(v.1.4.0), farver(v.2.0.1), zoo(v.1.8-6), hwriter(v.1.3.2), jsonlite(v.1.6), crosstalk(v.1.0.0), BiocParallel(v.1.20.0), RCurl(v.1.95-4.12), GenomeInfoDbData(v.1.2.2), leaps(v.3.0), Matrix(v.1.2-17), Rcpp(v.1.0.3), munsell(v.0.5.0), S4Vectors(v.0.24.0), lifecycle(v.0.1.0), scatterplot3d(v.0.3-41), stringi(v.1.4.3), yaml(v.2.2.0), MASS(v.7.3-51.4), SummarizedExperiment(v.1.16.0), zlibbioc(v.1.32.0), plyr(v.1.8.4), grid(v.3.6.1), promises(v.1.1.0), crayon(v.1.3.4), lattice(v.0.20-38), Biostrings(v.2.54.0), hms(v.0.5.2), zeallot(v.0.1.0), knitr(v.1.26), pillar(v.1.4.2), GenomicRanges(v.1.38.0), reshape2(v.1.4.3), stats4(v.3.6.1), glue(v.1.3.1), evaluate(v.0.14), ShortRead(v.1.44.0), latticeExtra(v.0.6-28), data.table(v.1.12.6), httpuv(v.1.5.2), vctrs(v.0.2.0), gtable(v.0.3.0), purrr(v.0.3.3), tidyr(v.1.0.0), assertthat(v.0.2.1), xfun(v.0.11), mime(v.0.7), xtable(v.1.8-4), later(v.1.0.0), viridisLite(v.0.3.0), truncnorm(v.1.0-8), GenomicAlignments(v.1.22.1), IRanges(v.2.20.0), cluster(v.2.1.0) and ellipsis(v.0.3.0)